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Items: 24

1.

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VL, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger MF, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu Z.

Genome Biol. 2014 Sep 23;15(9):459. doi: 10.1186/s13059-014-0459-2.

2.

Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence.

Wattam AR, Foster JT, Mane SP, Beckstrom-Sternberg SM, Beckstrom-Sternberg JM, Dickerman AW, Keim P, Pearson T, Shukla M, Ward DV, Williams KP, Sobral BW, Tsolis RM, Whatmore AM, O'Callaghan D.

J Bacteriol. 2014 Mar;196(5):920-30. doi: 10.1128/JB.01091-13. Epub 2013 Dec 13.

3.

Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance.

Maldonado-Contreras A, Mane SP, Zhang XS, Pericchi L, Alarcón T, Contreras M, Linz B, Blaser MJ, Domínguez-Bello MG.

BMC Microbiol. 2013 Sep 19;13:211. doi: 10.1186/1471-2180-13-211. Erratum in: BMC Microbiol. 2014;14:122.

4.

Helicobacter pylori colonization ameliorates glucose homeostasis in mice through a PPAR γ-dependent mechanism.

Bassaganya-Riera J, Dominguez-Bello MG, Kronsteiner B, Carbo A, Lu P, Viladomiu M, Pedragosa M, Zhang X, Sobral BW, Mane SP, Mohapatra SK, Horne WT, Guri AJ, Groeschl M, Lopez-Velasco G, Hontecillas R.

PLoS One. 2012;7(11):e50069. doi: 10.1371/journal.pone.0050069. Epub 2012 Nov 15.

5.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC.

MBio. 2012 Nov 6;3(5):e00246-11. doi: 10.1128/mBio.00388-12.

6.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC.

MBio. 2012 Aug 28;3(5):e00246-12. doi: 10.1128/mBio.00246-12. Print 2012. Erratum in: MBio. 2012 Nov-Dec;3(6):e00388-12.

7.

Genomic comparison between a virulent type A1 strain of Francisella tularensis and its attenuated O-antigen mutant.

Modise T, Ryder C, Mane SP, Bandara AB, Jensen RV, Inzana TJ.

J Bacteriol. 2012 May;194(10):2775-6. doi: 10.1128/JB.00152-12.

8.

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

Rodgers-Melnick E, Mane SP, Dharmawardhana P, Slavov GT, Crasta OR, Strauss SH, Brunner AM, Difazio SP.

Genome Res. 2012 Jan;22(1):95-105. doi: 10.1101/gr.125146.111. Epub 2011 Oct 5.

9.

PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species.

Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, Nordberg EK, Scott M, Schulman JR, Snyder EE, Sullivan DE, Wang C, Warren A, Williams KP, Xue T, Yoo HS, Zhang C, Zhang Y, Will R, Kenyon RW, Sobral BW.

Infect Immun. 2011 Nov;79(11):4286-98. doi: 10.1128/IAI.00207-11. Epub 2011 Sep 6. Review.

10.

Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rRNA amplicons.

Lopez-Velasco G, Welbaum GE, Boyer RR, Mane SP, Ponder MA.

J Appl Microbiol. 2011 May;110(5):1203-14. doi: 10.1111/j.1365-2672.2011.04969.x. Epub 2011 Mar 3.

11.

Microbial diversity in saliva of oral squamous cell carcinoma.

Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D.

FEMS Immunol Med Microbiol. 2011 Apr;61(3):269-77. doi: 10.1111/j.1574-695X.2010.00773.x. Epub 2011 Feb 1.

12.

The genome of woodland strawberry (Fragaria vesca).

Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM.

Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26.

13.

Analysis of high-throughput sequencing data.

Mane SP, Modise T, Sobral BW.

Methods Mol Biol. 2011;678:1-11. doi: 10.1007/978-1-60761-682-5_1.

PMID:
20931368
14.

Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses.

Mane SP, Dominguez-Bello MG, Blaser MJ, Sobral BW, Hontecillas R, Skoneczka J, Mohapatra SK, Crasta OR, Evans C, Modise T, Shallom S, Shukla M, Varon C, Mégraud F, Maldonado-Contreras AL, Williams KP, Bassaganya-Riera J.

J Bacteriol. 2010 Jun;192(12):3078-92. doi: 10.1128/JB.00063-10. Epub 2010 Apr 16.

15.

Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing.

Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, Hutchison SK, Harkins TT, Thierry-Mieg D, Thierry-Mieg J, Jensen RV.

BMC Genomics. 2009 Jun 12;10:264. doi: 10.1186/1471-2164-10-264.

16.

Targeted development of registries of biological parts.

Peccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, DeLalla EC, Evans C, Folkerts O, Lyons BM, Mane SP, Shelton R, Sweede MA, Waldon SA.

PLoS One. 2008 Jul 16;3(7):e2671. doi: 10.1371/journal.pone.0002671.

17.

Physiological and molecular adaptations to drought in Andean potato genotypes.

Vasquez-Robinet C, Mane SP, Ulanov AV, Watkinson JI, Stromberg VK, De Koeyer D, Schafleitner R, Willmot DB, Bonierbale M, Bohnert HJ, Grene R.

J Exp Bot. 2008;59(8):2109-23. doi: 10.1093/jxb/ern073.

18.

Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.

Crasta OR, Folkerts O, Fei Z, Mane SP, Evans C, Martino-Catt S, Bricker B, Yu G, Du L, Sobral BW.

PLoS One. 2008 May 14;3(5):e2193. doi: 10.1371/journal.pone.0002193.

19.

A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case.

Yu GX, Snyder EE, Boyle SM, Crasta OR, Czar M, Mane SP, Purkayastha A, Sobral B, Setubal JC.

Nucleic Acids Res. 2007;35(12):3953-62. Epub 2007 Jun 6.

20.

Early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis.

Mane SP, Vasquez-Robinet C, Sioson AA, Heath LS, Grene R.

J Exp Bot. 2007;58(2):241-52.

PMID:
17261695
21.

PATRIC: the VBI PathoSystems Resource Integration Center.

Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BW.

Nucleic Acids Res. 2007 Jan;35(Database issue):D401-6. Epub 2006 Nov 16.

22.

Effects of chronic ozone exposure on gene expression in Arabidopsis thaliana ecotypes and in Thellungiella halophila.

Li P, Mane SP, Sioson AA, Robinet CV, Heath LS, Bohnert HJ, Grene R.

Plant Cell Environ. 2006 May;29(5):854-68. Erratum in: Plant Cell Environ. 2006 Jul;29(7):1460-1.

23.

Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field.

Li P, Sioson A, Mane SP, Ulanov A, Grothaus G, Heath LS, Murali TM, Bohnert HJ, Grene R.

Plant Mol Biol. 2006 Nov;62(4-5):593-609. Epub 2006 Aug 29.

PMID:
16941220
24.

The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison.

Sioson AA, Mane SP, Li P, Sha W, Heath LS, Bohnert HJ, Grene R.

BMC Bioinformatics. 2006 Apr 20;7:215.

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